Abstract: In order to fully understand the academic influence of the papers published in the Journal of Yunnan University (Natural Science Edition) in a certain period of time, the highly cited papers published in the journal from 2007 to 2016 were selected by using the data from the CNKI Chinese Citation Database (CCD). Statistical analysis was carried out according to the subject, the professional and educational background of the first author, the institutions of the first author, the number of author and the fund projects. The results showed that biology was the subject with the most sources of the highly cited papers, and 38.32% of highly cited papers were from Yunnan University, and the largest number of authors was 3—5, and 98.13% of highly cited papers were supported by funds. Finally, some suggestions were put forward from the following aspects: attaching importance to advantages and special columns, giving full play to the role of editorial committee, paying attention to review papers, strengthening the training of young authors, and providing high-quality services.